Reference

Internal Objetos usados solo en las viñetas.
interpro_INTERPRO_long	interpro_INTERPRO_long
interpro_INTERPRO_profile	interpro_INTERPRO_profile
interpro_KEGG_long	interpro_KEGG_long
interpro_map	interpro_map
interpro_pfam_long	interpro_pfam_long
interpro_pfam_profile	interpro_pfam_profile
ko_bin_mapp	Output of mapping_ko
ko_bin_table	Output of read_ko
metadata	Metadata
rbims	Main Rbims
read_ko_shiny()	Read the output of KofamScan/KofamKoala or KAAS.
EC_picrust2	EC abundances predicted with PICRUSt2
KO_picrust2	KO abundances predicted with PICRUSt2
pathway_picrust2	Pathway-level predictions with PICRUSt2
KEGG analysis Functions used for KEGG
read_ko()	Read the output of KofamScan/KofamKoala or KAAS.
mapping_ko()	Maps KOs to the KEGG database.
read_picrust2()	Read the output of PICRUSt2
write_metabolism()	Metabolism table
InterProScan analysis Functions used for InterProScan analysis
read_interpro()	Extract abundance profile of InterProScan output.
MEROPS analysis Functions used for MEROPS analysis
read_merops()	Read the output of merops and extract abundance profile
dbCAN analysis Functions used for dbCAN analysis
read_dbcan3()	Read the output of dbCAN and extract abundance profile
Manipulate KEGG/InterproScan profile Functions used to manipulate the KEGG/InterproScan profile
get_subset_unique()	Unique abundance profile.
get_subset_pca()	Metabolism PCA
get_subset_pathway()	Subsets the mapped KO table based on pathways.
calc_binary()	Calculate presence/absence.
calc_percentage()	Calculate the percentage.
Plot KEGG/InterproScan profile Functions used to plot the KEGG/InterproScan profile
plot_bubble()	Bubble plot of features (KO/pathways/modules) per bin
plot_heatmap()	Heatmap
Pathway Analysis
calc_pathway_directional_bias()	Calculate pathway-level directional bias (binomial test)
plot_pathway_directional_bias()	Plot pathway-level directional bias (proportion + CI)
Discriminant Features
get_discriminant_features()	Identify discriminant features across MAGs
get_subset_discriminant()	Filter feature table by discriminant score
plot_disc_effect()	Plot differential effect for discriminant features
plot_disc_heatmap()	Plot discriminant features as Group × Feature heatmap
Utilities
make_ko_dictionary()	Build a KO annotation dictionary from an rbims KEGG table